X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=README.md;fp=README.md;h=9fe0297fd769b705ba0bf1969046c73d47f869af;hb=c729fa33c6e2f9e3e1b374c66a55265525e7d974;hp=f6b5ec857f44861c1cd4d5d62b483738e511833d;hpb=f054dfb3f9bb35d4043534ea88e1f5fa8e7eb2ea;p=rsem.git

diff --git a/README.md b/README.md
index f6b5ec8..9fe0297 100644
--- a/README.md
+++ b/README.md
@@ -304,11 +304,14 @@ __N:__ The total number of reads to be simulated. If 'rsem-calculate-expression'
 
 __output_name:__ Prefix for all output files.   
 
+__--seed seed:__ Set seed for the random number generator used in simulation. The seed should be a 32-bit unsigned integer.
+
 __-q:__ Set it will stop outputting intermediate information.   
 
 ### Outputs:
 
 output_name.sim.isoforms.results, output_name.sim.genes.results: Expression levels estimated by counting where each simulated read comes from.
+output_name.sim.alleles.results: Allele-specific expression levels estimated by counting where each simulated read comes from.
 
 output_name.fa if single-end without quality score;   
 output_name.fq if single-end with quality score;